I am analyzing BLAST results from total RNA NGS, pair ends. This BLAST results was performed against the ssRNA virus database download from NCBI.
I filtered those read data whose paired ends uniquely matched a single virus and I have both (removing single reads).
Moreover, based on the
send values from a unique virus in each library I calculated the difference (ssdif) of the lowest (sstart) of the highest (send) value that I got in the BLAST results,
for example: If I got 4 reads that match against one virus in one library (2 reads with pair ends) I got the lowest
sstart and the highest
send for these four hits.
Then, I calculated the coverage using the ssdif;
coverage=(ssdif/genome length for that virus) * 100
After I calculate the coverage for each virus in each library based of the BLAST results I calculated the mean coverage for each genus and for each family of all viruses detected in my analysis.
- Does it make sense the way that I calculated the coverage? I would like to filter my data for those viruses that have similar or higher coverage to the genus or family (previously calculated)
- Based on what taxonomic level does it make more sense filter them?
Thanks in advance